Japan is expensive but there are semi-affordable ways to travel there.
The New Koyo Hotel (
www.newkoyo.jp), for instance, will set you back only about $20 a night and is not that bad. It's in Tokyo. You may be able to find similarly cheap lodging in other places in Japan but I don't know any names off hand.
The JR Rail Pass costs about $250 / week. If you're only going to be in one small region (ie. a city) of Japan you're better off paying as you go.
Plane tickets to Japan are usually most expensive during the winter (I got round trip tickets for December from the bay area for about $800 -- other seasons cost more like $500). Early-mid April is the best time to visit Japan, if you can. June-July is rainy season, and August is really hot.
I posted some other info about visiting Japan in this thread:
http://www.tfproject.org/tfp/showthr...threadid=31554
What specifically are you interested in seeing?